Is CHD3 p.Arg933fs (c.2798_2799del) pathogenic?

CHD3 p.Arg933fs (c.27982799del) is classified Likely pathogenic in CHD3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-04). Absent from gnomAD; Associated with Snijders Blok-Campeau syndrome.

What condition is associated with CHD3 p.Arg933fs (c.2798_2799del)?

CHD3 p.Arg933fs (c.2798_2799del) is associated with Snijders Blok-Campeau syndrome (ClinVar).

How common is CHD3 p.Arg933fs (c.2798_2799del) in the general population?

CHD3 p.Arg933fs (c.2798_2799del) is absent from gnomAD (gnomAD).

CHD3 p.Arg933fs

c.2798_2799del · rs2544948285 · VCV2572183

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Snijders Blok-Campeau syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 17 of 40
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	GERP 1.9, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CHD3
Protein: p.Arg933fs
Coding: c.2798_2799del
MANE Select: NM_001005273
dbSNP: rs2544948285
Type: Microsatellite
Location: chr17:7900400 (GRCh38)
Gene constraint: LOEUF 0.257 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.21
Residue 933: a UniProt-annotated variant site (in snibcps)

Full CHD3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Snijders Blok-Campeau syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CHD3 p.Gln1438fs Likely pathogenic ★ same condition
CHD3 p.Val7fs Pathogenic ★ same condition
CHD3 p.Gly1109del Uncertain significance ★ same condition
CHD3 p.Pro82_Leu83insProPro Uncertain significance ★ same condition
CHD3 c.4073-2A>C Likely pathogenic ★★ same condition
CHD3 p.Arg1078Gln Pathogenic/Likely pathogenic ★★ same condition
CHD3 p.Arg1121Pro Pathogenic/Likely pathogenic ★★ same condition
CHD3 p.Arg1169Gln Pathogenic/Likely pathogenic ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/chd3-p-arg933fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown